Root's Guardian
by The-Programmer
Summary: At the age of eight Danzo convinces Naruto to join ROOT. From then on he has sworn to protect Konoha from the shadows and never attends the academy. How will this affect the rest of Naruto's life? Read to find out. Rated T for now, will probably change. I'm back.
1. Welcome To ROOT

**Disclaimer: I do not own Naruto**

**_AN_**: **This is my first story. No flaming. It is still undecided if I will put pairings in is a poll on my profile for it.  
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****(Poll closes** chapter5 )**

** If I do it will be boy/girl pairings only.**

**Please review.  
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_Welcome to ROOT_**  
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It was a calm and peaceful morning in Konoha, that is of course you weren't a certain vendor or an eight year-old orphan. Naruto was running down the street carrying a bento box in his hand. The problem? He had just stolen it from a merchant's cart that had attracted the starving boy's attention. "Hey! Give it back! That's mine!" The vendor yelled to no avail.  
>After about fifteen minutes of chasing the blond soon-to-be ninja had evaded the old salesman and found a nice spot at the playground to eat his "discounted" lunch in peace. Or so he thought.<br>"Hey! It's the demon brat!" One villager called, throwing a stone he had freshly picked up from the ground.

Naruto held back his tongue and tears, but was assaulted with more stones from random citizens of Konohagakure. At that point he decided it would be best if he ran for the Hokage's office, at which he knew the he would at least be safe from harm. He ran as far as he could, ignoring the burning in his lungs, using his sleeve to wipe his eyes, hoping that with some luck he would make it to his safe haven. Luck was apparently not on his side when he tripped on a root and a mob formed around him, all whom which were wielding makeshift weapons, hoping to finish what they thought the Fourth Hokage had started, when all of a sudden an old voice commanded.

"Stop, or you will all be arrested in accordance with the Third's law.  
>He opened his eyes and stopped sobbing for a moment. A man with a walking stick and strange clothing appeared with a group of masked ninja. He had a bandage all over the right side of his head.<p>

"P...please don't hurt me anymore." Naruto said.

"Don't worry, if anything it should be these villagers who should be hurt for bringing harm to a citizen of Konoha." Said the old war-hawk

"The...village hates me. They call me a monster."

"I heard. Let me guess your name is Uzumaki, Naruto, right?"

"How did you know?"

"My name's Danzo. I can teach you how to defend yourself. How about it?"

"Y-yeah! That'd be great."

"First you have to do something for me though."

"Sure whatever you want."

"I knew you'd say that. Let's leave this discuss at another time though, for now go home and take a shower, I'll stay behind and handle this."

With this Naruto left to his run-down apartment.

"Danzo-sama what should we do with these villagers?" asked a ROOT agent

"Execute them." The elder nin commanded

"Yes sir." replied the ROOT nin.

* * *

><p>Naruto stepped out of the steamy shower and wrapped his towel around him. He scrubbed his wet hair and body down with the towel, and clothed himself. He had mixed feelings and was thinking about what Danzo wanted him to do. Suddenly he heard a noise and sprung behind his table, knife in hand.<br>"Do not fret my boy, it is only me Danzo, and some of my guards." a voice spoke out from the doorway

"H..how do you know where I live?" asked the freshly bathed blond.

"I had some nin follow you home to make sure you got home safely."answered Danzo

"Why would you do that?"

"I need you in top shape if you want to learn how to protect yourself."

"Sure, but earlier you mentioned that I needed to do something for me."

"I will tell you about that later. But first you must promise to keep everything a secret."

"I promise, and I intend to keep all my promises."

"Is that your nindo?"

"My what?"

"A nindo is a personal code on which ninjas base their lives off."

"Then yes, this is my personal nindo."

"Good." the war hawk finished. And in a blur stabbed Naruto in the neck with a sebon.

* * *

><p>Naruto awoke with a yawn. His eyes watered, and his skin stretched drastically, putting his face into an immediate discomfort. He blinked a few times, which caused his vision to blur and settle.<p>

They room Naruto found himself in was rather plain, the walls were bamboo, along with the floors, there was a single bedroll, a small desk, which contained paper, ink, and a single candle, and two doors. The only noticeable thing was the leaf symbol that seemed burned into the floor.

"Where the hell am I?' Naruto thought aloud.

"You are in the main ROOT base." a voice replied.

"Ahhh!" said the Blondie as he spun around to meet who was talking.

"Danzo, why did you attack me and bring me here?" Naruto continued.

"I just knocked you out so that I could explain, what I want in return of teaching you." the war-hawk explained.

"Why couldn't we just walk here instead of you stabbing me?"

"Well you see, I needed to be sure I could trust you before explaining everything to you."

"So you stabbed me instead." Naruto deadpanned.

"Yes, you see you cannot know the location of this base until I am completely sure that you would be loyal to ROOT and its cause."

"What's ROOT?" the blond questioned.

"ROOT is an group of ninja who have promised to protect the village from the shadows. Do missions that are usually refused by the Hokage and his advisors. Its kind of like our nindo" Danzo stated.

"Why would the old-man refuse a mission?"

"Either the death-toll would be to high, or its morally wrong."

"Wait, you're talking about me being a ninja, I haven't even started the academy."

"You will be receiving training from two of my jonin."

"Why would I want to protect a village, that wants me dead?" Naruto asked, starting to get angry.

"Because, it is what your father would do."

"NANI! You know who my dad was?" Who was he? Was he a great ninja? Who's my mom? Do I belong to a clan."

"I would love to answer your questions, but you need to prove that you can handle this information. I will tell you he was probably one of the best shinobi I had ever met."

"How do I do that?"

"By joining ROOT and swearing you loyalty to our group."

"I will join then, to find more about my past. I swear to ROOT that I will always be loyal. This is my promise of a lifetime."

"Welcome to ROOT." Danzo smiled, and held his hand out to shake Naruto's.

_**AN:**_ **Yes I know its short. Hopefully the other chapters will be longer**.


	2. Briefing

_**AN:**__** No flames please, but do review. **_

_**There is an open poll on pairings for this story on my profile.**_

_**Danzo knows about Naruto's Heritage in this story.**_

_** Happy reading!  
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Briefing

"Now that you are officially part of ROOT, let me explain how things will work for you. You will have training everyday for eight hours, the first four will be physical, the other four mental. During your physical training you will have a partner, whom of which I will decide later. You will have two senseis during the first four hours will train you in weapon mastery, chakra control, strength training, assassination techniques, stealth, and jutsus. The first two hours of your mental training will be in torture techniques and poisons, and on how resist torture and poisons. The third hour will be spent learning important history..." Danzo was saying before being interrupted by Naruto.

"Awww... I have to learn history?" The blond complained.

"Yes, you can't protect yourself if you have no idea what it is. Now as I was saying, The fourth our will be spent reading about and understanding how seals and jutsus work. Hyo will be your sensei for the mental section, but you will find out your other two tomorrow along with who your partner is going to be. After this you have time to yourself." Danzo continued. "You will have breakfast as soon as you wake up, lunch between your two training sessions, and dinner is at eight. You are expected to be in bed by eleven unless you are on patrol or a mission. Don't worry though I won't have you doing missions for the first four years that way you may have proper training. I will send Hyo to show you around. This is your room for the rest of your time with ROOT. In the closet you will find a cloak for the cold, a ANBU mask, a half face mask, black ninja pants, a black shirt, training weights, ninja boots, fingerless gloves, standard ninja equipment, and a tanto. Any questions?" Danzo finished.

"Do I have to wear both mask?" Naruto asked.

"Ah yes, let me explain about your masks. Your masks are not only to protect your identity, but to inform other members that you are one of them, which can be a blessing depending on your situation. The half mask is to wear under the other mask in-case it gets damaged on a mission. There will be some missions that it is required that you don't wear either mask, if thats the case you are expected to have your mask hidden away on your persona at all times." The older ninja informed the ninja-in-training.

"What about the academy and the Hokage?" Naruto asked.

"You will still make visits to the Hokage, just to keep up appearances, and you will attend the afternoon classes at the academy. But under no circumstance can you tell the Hokage about your training or ROOT."

"Why not?"

"Root was officially disbanded at some point in the past, but remained active as an underground organization. The organization's top priority is its secrecy, and most of its missions are carried out in the dark - autonomous of Konoha's authority, but for the benefit of Konoha." explained Danzo.

"Why was it disbanded?"

"Well some of the missions we did may have be less than respectable, and the third Hokage thought he could run Konohagakure without them, and also due to the fact of the emotion conditioning we did, but for this batch of operatives we decided to do away with it as a temporary experiment to see if we could use emotions as a strength instead of seeing it as a weakness"

"Ohhh. Can I ask you another question, why does the village hate me, I know I prank people and I steal food, but thats because the vendors always seem to raise prices right when I get there. And the rest of the village just despises me and spits on me." Naruto asked and explained.

"Hmm, might as well tell you now. Do you know about the nine-tails?" Danzo asked

"Yes, but what does that have to do with me?" Naruto asked, starting to get scared.

"You see the Kyuubi couldn't be killed because it is a mass of chakra, and the Fourth Hokage knew that so he took a child, and sealed it in it, and Naruto that child is you."

"So am the Kyuubi?"

"No, let me explain it this way." said Danzo as he picked up the candle from the table and pulled out a sealing scroll from his pocket. He then proceeded to seal the candle into the scroll.

"Okay, let me ask you, is the scroll the candle?" the old war-hawk asked.

"No, the candle is just sealed inside." answered the blond jinchuriki.

"Exactly. You are not the demon, but only is jailer and warden combined in one." Answered Danzo.

"So, I'm just like the scroll?"

"Yes you're the scroll but unlike the scroll you can use the object sealed within you abilities. As we will practice during your training, but for now, I must leave. Get some rest for tomorrow is going to be a long day. Goodnight Naruto." Danzo finished.

"Goodnight, Danzo-sama." Said Naruto already moving to turn out the candle.

"Oh, and one last thing. Be sure you're up by six tomorrow."

"Yes, Danzo-sama."

_**AN:**__** I Know it was another short chapter, but I'm already halfway done with chapter 3 and it is already longer then this one. **_

_**Remember to vote on the poll on my profile and remember to review!**_

_**P.S. Expect the next chapter on Saturday!  
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	3. Bad Introductions

**Disclaimer: I do not own Naruto**

**_AN_**: **This is my first story. No flaming. It is still undecided if I will put pairings in is a poll on my profile for it. **

****(Poll closes** chapter5 )**

** If I do it will be boy/girl pairings only.**

**Please review. **

"Get up maggot!" Yelled a deep, rough voice, as Naruto was sent flying across the room along with the rest of the bed.

"What the hell?" Questioned a now startled blonde, struggling to get in a defensive stance.

"Pathetic." Said the still unknown man, as he charged towards the fox container. Punching naruto in the face right through his guard, sending him through several of the bases walls, finally stopping in a standard dojo.

"I can't believe I got stuck training this brat for the next two years." Spoke the assailant following naruto through the holes.

"Hey, I'm not a brat." Countered the young blonde.

"Now, now, don't both of you have a quite a temper." Spoke a silky female voice, coming from the door.

"Who asked you, Mika? Plus aren't you banned from training new kids."

"I got ordered here, by Danzo-Sama himself. Plus someone needs to make sure the kids gets some smarter, least he end up like you." Spoke Mika.

"Yes, and I expect both of you to train Young Naruto here to his full potential." The old war hawk said from the doorway, looking slightly irritated, startling both of the veteran Root agents.

"Sorry Danzo-sama" both replied looking down in shame.

"Wait. I'm supposed to get training from this psychopath, and this old hag for the next two years!" Exclaimed the jinjuriki.

"Old! I'm barely 24 you dumb brat!" Shouted Mika.

"Mika, restraint! Yes, Naruto. These our two of our best operatives, who haven't undergone emotion training either. They are the reason for my choice. " Replied Danzo. "Katuka here is one of the best fighters we have and an expert swordsman, and Mika is the Root trainer in interrogation and stealth." "

I guess that's ok then." Naruto said. "Good. That concludes today's morning session. You have meet both of your sensei's for you physical training, Hyo should be here in a couple of minutes to give you a tour of the facilities and answer any questions you have. Mika, Katuka, come with me, something has come up that requires our immediate attention." Spoke Root's leader as he walked out the door with both of said agents following him.

"Great, so I'm stuck here until this Hyo guy comes." Muttered blondie.

"I wouldn't talk like that if I was you, you may never know who might be listening." Called an smooth voice from the hole he had made when Katuka punched him.

"I suppose your Hyo." Stated naruto. "I'm surprised you weren't more shocked. Normally people jump when I appear without notice."

"Yeah, well when you live on the streets as long as I have not much phases you anymore."

"Well look who's being a little emo right now."

"Hey I'm not emo!"

"Whatever let's get this tour done with. The academy starts in a couple hours. Plus, its a giant base." Said Hyo motioning naruto to follow him. "

* * *

><p><em><strong>A couple of hours later..<strong>_

Well that's about all of it. Are you ready to head to the academy our do you want to change, because you look pretty stupid in orange."

"Hey that's all I could get. They just don't give out free clothes on the streets."

"Whatever, go back and shower. I'll be at your room in thirty minutes to escort you to the village walls. From there you're on your own, till after class."

* * *

><p><strong><em>Twenty-seven minutes later..<em>**

Naruto stepped out of the shower, putting on the clothes that he had in his closet. He never owned a closet before. Much less a room. Now he did. . . "Are you ready for school yet?" Asked Hyo through the door.

"Yeah." The blonde root agent replied. Slipping the root mask into his pocket while putting on the half-mask. Hyo moved out of the way while Naruto stepped out of the door.

"Let's go." Hyo said as the dashed through the halls, and outside.

* * *

><p><em><strong>AN: Sorry for the long wait and short chapter, I typed all of this using only my phone's notes app, but i just bought my new laptop so expect more soon. **_


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